How to extract info from a chemical formula

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Patrick Knapp
Patrick Knapp 2011-8-12
回答： phenan08 2023-1-26
Hi All, I want to break down a chemical formula into its constituents. For example: Silicon Dioxide = SiO2 I want to take the string 'SiO2' and parse it so that I know I have 1 silicon and 2 oxygens. I want to do this for more complex compounds as well, say Polyimide which is 'C22H10N2O5'. So I need to handle upper case and lower case letters, and 1 or 2 digit numbers. Any help would be much appreciated.
Pat

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回答（4 个）

Fangjun Jiang
Fangjun Jiang 2011-8-12
Use the combination of isstrprop() and regexp() might help. You need to provide more examples and explain what you want.
str='C22H10N2O5'
num=regexp(str,'\d+','match')
isstrprop(str,'alpha')
isstrprop(str,'digit')
isstrprop(str,'upper')
One solution:
str='C22H10PuCrN2O5';
[EleList,Trash,EleEnd]=regexp(str,['[','A':'Z','][','a':'z',']?'],'match');
[Num,NumStart]=regexp(str,'\d+','match');
NumList=ones(size(EleList));
Index=ismember(EleEnd+1,NumStart);
NumList(Index)=cellfun(@str2num,Num);
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Fangjun Jiang
Fangjun Jiang 2011-8-12
Please refresh my memory. Is it true that the element can only have two or one letter? If it is two-letter, is it true that the first letter is always uppercase and the second letter is lowcase?
Paulo Silva
Paulo Silva 2011-8-12
look at any periodic table that you might find online, all symbols should be there

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Paulo Silva
Paulo Silva 2011-8-12
That's not easy to do, for example not all formulas have the constituents separated by a number, you also need to have all possible constituents in a list so you can identify them in any formula and after it check if there's a number after each constituents.
Please search in the File Exchange ,you might get lucky and find it already done by someone.
  1 个评论
Kelly Kearney
Kelly Kearney 2011-8-12
Well, assuming he's not dealing with any of those U** elements at the upper end of the periodic table, then all elements consist of either one capital letter or a capital and lowercase letter. So it should be pretty easy to pick those out. Will you always have the base formula, or will it be arranged structurally (i.e. Si(OH)4, or SiO4H4?)

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Patrick Knapp
Patrick Knapp 2011-8-12
I figured it out. Thanks for the help Fangjun!
str = 'SiO2';
num=regexp(str,'\d+','match'); % cell array containing the numbers
D = isstrprop(str,'digit'); %logical array giving location of numbers
U = isstrprop(str,'upper'); %logical giving location of upper case alphas
L = isstrprop(str,'lower'); %logical giving location of lower case alphas
NumElem = sum(U); %number of upper case alphas == number of elements in formula
Formula = struct('element',{},'quantity',{}); %initialize output
%%Loop through formula to extract quantities
n = 1;
num_counter = 1;
for i = 1:NumElem
if U(n)
if U(n) && L(n+1)
Formula(i).element = str(n:n+1);
n = n+2;
if ~D(n)
Formula(i).quantity = 1;
elseif D(n)
Formula(i).quantity = str2num(num{num_counter}); %#ok<*ST2NM>
n = n+length(num{num_counter});
num_counter = num_counter+1;
end
elseif U(n) && ~L(n+1)
Formula(i).element = str(n);
n = n+1;
if D(n)
Formula(i).quantity = str2num(num{num_counter});
n = n+length(num{num_counter});
num_counter = num_counter+1;
elseif ~D(n)
Formula(i).quantity = 1;
end
end
else
n = n+1;
end
end
  1 个评论
Fangjun Jiang
Fangjun Jiang 2011-8-12
Nice! I couldn't resist coming up with a no-loop solution. See my updated answer.

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phenan08
phenan08 2023-1-26
If it can help, I wrote a formula string parser to determine the composition of a molecule, element by element.
https://fr.mathworks.com/matlabcentral/fileexchange/117670-parse_formula
It is possible to use semi-developped formulas, and the script returns 4 outputs: the raw molecular formula, the composition table (the different elements with their counts), the average MW and the monoisotopic mass.

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